Mus81-Eme1 Are Essential Components of a Holliday Junction Resolvase Michael N. Boddy, Pierre-Henri L. Gaillard, W.Hayes McDonald, Paul Shanahan, John R. Yates, Paul Russell  Cell  Volume 107, Issue 4, Pages 537-548 (November 2001) DOI: 10.1016/S0092-8674(01)00536-0

Figure 1 Purification of Mus81-TAP and Identification of Eme1 (A) Silver-stained SDS gel of Mus81-TAP purification. TEV eluate; TEV cleavage products from IgG column. CaM flow; flow through from TEV eluate passed over calmodulin affinity column. Wash 1,2; calmodulin column washes. CaM eluate; eluate from the calmodulin column used for tandem mass spectrometry. The position of Mus81 is indicated and Eme1 is expected to run just below this position. However, we have not established which of these faint bands represents Eme1. (B) Peptide sequence of Eme1. Eme1 peptides obtained by mass spectrometry are shown in red. The region of Eme1 found to interact with Mus81 in the yeast two-hybrid screen is underlined. Predicted coiled-coil domain is indicated. (C) Confirmation of in vivo interaction of Mus81 with Eme1. GST-Mus81 fusion proteins; “F”, full; “N”, N terminus and “C”, C terminus were expressed in a strain expressing HA epitope tagged Eme1. HA-Eme1 is detected in GST-Mus81 “F” and “C” but not “N” precipitates isolated with GSH-Sepharose. WCL, whole cell lysate. (D) Interaction of Eme1 with the Mus81DD. GST-Mus81DD “F” and “C” were expressed in an HA-Eme1 strain. HA-Eme1 coprecipitated with both GST-Mus81DD proteins. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 2 Mus81 and Eme1 Function in the Same Pathways of UV Resistance (A) Codependent functions of Mus81 and Eme1 for tolerance of irreparable UV lesions. UV sensitivity in a uve1 rad13 background was enhanced by mus81 and eme1 mutations. The quadruple mutant was no more UV sensitive than either triple mutant. (B) In a repair proficient background (uve1+ rad13+), mus81 and eme1 mutations enhanced UV sensitivity and the mus81 eme1 double mutant was no more UV sensitive than either single mutant. (C) The mus81-DD mutant was as UV sensitive as the mus81 delete strain. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 3 Meiotic Defects of mus81 and eme1 Mutants (A) Spores from mus81 and eme1 asci exhibit very poor viability. This defect is rescued by rec6 and rec12 mutations that prevent meiotic recombination. All diploids were homozygous with the exception of the mus81−/mus81+ heterozygote. (B) DNA segregation defects in mus81 asci. WT, mus81 and rhp51 asci were visualized by DIC microscopy to show spores (upper panels) and stained with DAPI to visualize DNA (lower panels). Mature asci in each DIC panel are outlined with a dashed line. Arrowheads indicate aberrant meiotic products in mus81 asci. (C) The majority of mus81 asci contain a single focus of DNA. The number of discreet DAPI stained foci per ascus was ascertained. Approximately 100 mature asci were counted for each strain. (D) The segregation defect observed in mus81 meioses is corrected by expression of RusA. mus81 mutants expressing RusA were mated and mature asci were examined microscopically. The number of discreet DAPI stained foci per ascus was ascertained. (E) The low spore viability resulting from mus81 meioses is substantially rescued by RusA. mus81 mutants carrying pRep1, pRep1-RusA, or catalytically dead pRep1-RusA-D70N were mated and the resultant spore viabilities determined. Data shown are representative of four independent experiments. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 4 Mus81 and Eme1 Are Components of a Structure-Specific Endonuclease (A) Schematic representations of the structure of each DNA substrate are shown above the gel. Each structure contains a 5′ labeled oligonucleotide X1 as indicated by the black dot. The DNA substrates were incubated with 0.5 μl and 6 μl of TEV-eluates obtained from the Mus81:TAP strain (lanes 3, 4, 9, 10, 15, 16), the mus81-DD:TAP mutant strain (lanes 5, 6, 11, 12, 17, 18), or the mus81:TAP eme1 mutant strain (lanes 7, 8, 13, 14, 19, 20). Reactions were analyzed on a 12% sequencing gel. Maxam-Gilbert G+A and T+C sequencing ladders derived from oligonucleotide X1 were run in parallel (lanes 1, 2, 21, 22). (B) The main sites of cleavage as determined from the Maxam-Gilbert sequencing ladders, are indicated by arrows on each DNA structure. The area shaded in gray represents the 12 bp homology region that allows the junction to migrate in X12 and PX12. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 5 Resolution of the X-Structure into Linear Duplex Products (A) The X12 and PX12 structures were incubated with 3 μl of either TEV-elution buffer (lanes 1, 4) or TEV-eluate obtained from the Mus81:TAP strain (lanes 2, 3, 5, 6). Reactions were carried out in the absence or the presence of ATP as indicated. Reaction products were analyzed on a native PAGE gel. Markers run in parallel indicate the migration of a Y structure (lane 7) and a linear duplex made by annealing oligonucleotide X1 to an oligonucleotide of complementary sequence (lane 8). (B) Schematic representation of products generated by cleavage of an X-structure on oligonucleotides 2 and 4 or 1 and 3. (C) Schematic representation of products generated by cleavage of the partial X-substrate. Cutting on oligonucleotide X1 (black arrowhead) generates double-strand/single-strand hybrids that migrate faster than a linear duplex made of full-length complementary oligonucleotides (A, lanes 5 and 6). Cutting on oligonucleotide X2 (gray arrowhead) generates a duplex product that bears a 5′ single-strand flap corresponding to part of oligonucleotide X4 and which should migrate slower than a linear duplex. No such product was detected, indicating that the partial X-substrate was preferentially cut on oligonucleotide X1 between the two juxtaposed duplex arms. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 6 Mapping of Cleavage Sites on Each Arm of Migratable and Fixed Junctions (A) Four different X12 structures, each labeled on a different oligonucleotide, were incubated with 3 μl of either TEV-elution buffer (lanes 1, 8, 9, 16) or TEV-eluate obtained from the Mus81:TAP strain (lanes 4, 5, 12, 13). Reactions were analyzed on a 12% sequencing gel along with Maxam-Gilbert sequencing ladders (lanes 2, 3, 6, 7, 10, 11, 14, 15). Note that 5 min reactions were used for mapping the cleavage sites because cuts in the heterology regions accumulated during longer incubations (data not shown). Cleavage sites are indicated on each arm of the X-structure. Closely symmetric sites on opposing strands across the junction that were found inside the region of homology are indicated by the black arrows. Nonsymmetric sites in the region of homology or sites mapped in the heterologous sequences are indicated by open arrows. (B) Cleavage sites generated on a fixed junction were mapped on four different X0-structures, each labeled on a different oligonucleotide. The main cleavage sites are indicated on each arm of the structure. (C) Cleavage products generated with X0 (lanes 2 and 3) and X12 (lanes 5 and 6) were analyzed on a native PAGE gel. A linear duplex control was run in lanes 1 and 4. The bracket alongside lane 3 indicates the diffuse migration of the linear duplex products generated with X0. The arrowhead alongside lane 6 indicates the position of the linear duplex products generated with X12. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)

Figure 7 Models for Roles of Mus81-Eme1 (A) An HJ formed at a collapsed replication fork is either reversed by Rqh1 type helicases in a nonrecombinogenic pathway or resolved by a Mus81-Eme1 dependent endonuclease in a recombinogenic pathway. (B) A “bubble” structure with symmetric double-strand/single-strand DNA junctions and juxtaposed duplex arms could constitute a favored substrate for Mus81-Eme1 dependent endonuclease. Cofactors might help to stabilize the open structure in vivo. Symmetric or closely symmetric cuts on opposing strands would be generated at the double-strand/single-strand DNA junctions and result in HJ resolution. Cell 2001 107, 537-548DOI: (10.1016/S0092-8674(01)00536-0)